[R-pkg-devel] Win-builder: Author field differs from that derived from Authors@R

asilief [aut, cph], Alex Kargovsky [aut, cph], Knut Franke >> [cph], Alexander Semke [cph], Tilman Benkert [cph], Kasper Peeters >> [cph], Russell Standish [cph], Ivan Krylov [cre, cph]' >> Authors@R: 'Miquel Garriga [aut, cph], Stefan Gerlach [aut, cph], >> Ion Vasilief

[R-pkg-devel] Robj: reading proprietary format - first time packaging

Hi! Not being able to find an R package that would let me import an Origin(R)[0] OPJ file, I found liborigin[1] and used Rcpp (thanks, Dirk Eddelbuettel!) to create the package which I titled Ropj[2]. Right now it only understands the absolute minimum of what I needed to import, but I intend to

Re: [R-pkg-devel] How to obtain intercept of intercept-only glm in Fortran?

On Fri, 10 May 2019 16:17:42 + "Wang, Zhu" wrote: > Are there any examples or links for me to follow through more closely? Calling R functions from C++ is described at and elsewhere in Rcpp documentation. An example follows:

Re: [R-pkg-devel] R CMD check ERROR (strange to me)

On Thu, 9 May 2019 23:19:46 + "Wang, Zhu" wrote: > I have encountered some strange error (see 00install.out). It seems to have been stripped by the attachment filter, and there are no compilation errors on my system. Can you include the relevant lines from 00install.out inline? -- Best

Re: [R-pkg-devel] Need help for Debian check error

On Tue, 30 Apr 2019 19:53:49 + "Zhang, Lixiang" wrote: > I don't know why is that happening and how should I fix it. Thanks a > lot for your help. The e-mail from CRAN also said, >> More details are given in the directory: followed by a link scrambled by your e-mail software. When you

Re: [R-pkg-devel] parallel computing slower than sequential computing

On Mon, 29 Apr 2019 23:44:42 + "Wang, Zhu" wrote: > sessionInfo() > R version 3.5.2 (2018-12-20) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 18.04.2 LTS Which BLAS implementation do you use? One popular implementation, OpenBLAS, spawns multiple threads to do some

Re: [R-pkg-devel] How to obtain intercept of intercept-only glm in Fortran?

On Sat, 4 May 2019 22:41:16 + "Wang, Zhu" wrote: > In an R package I would like to compute intercept for an > intercept-only GLM in a Fortran subroutine. If all else fails, you could use R API [*] to call coef(glm.fit(...)), though it might require writing a C or C++ wrapper to avoid

Re: [R-pkg-devel] "Progress reports" for examples in packages.

Could R CMD check be using valgrind to run the examples? Valgrind has to interpret CPU instructions manually to be able to warn about results of code execution depending on memory values it considers undefined, so it is much slower than execution on a real CPU. One way to verify that on a

Re: [R-pkg-devel] No protocol specified

On Fri, 23 Aug 2019 09:18:07 +0200 "Dr. rer. nat. Michael Thrun" wrote: >> No protocol specified > > Can anyone translate this note to me in a way that I know what the > issue is? I might be mistaken, but "No protocol specified" is an error frequently returned by an X server [*] when a

Re: [R-pkg-devel] please help understand an error in openMP statements

On Thu, 12 Sep 2019 16:12:17 -0500 Marcin Jurek wrote: > U_NZentries.cpp:258:19: error: ‘covparms’ not specified in enclosing > ‘parallel’ > 258 | covmat= MaternFun(dist,covparms) + diagmat(nug) ; // summation from > arma > | ~^~~ This might be a compiler

Re: [R-pkg-devel] "Additional issues" show WRITE outside an array

On Fri, 26 Jul 2019 01:50:36 -0500 Jiahuan ye wrote: > I am very confused what causes the ERROR. Your code on line 197 of src/min_wgss.cpp causes memory access outside the block that had been allocated for the best_change_point vector. I have not read the code in depth, but it looks like the

Re: [R-pkg-devel] debugging memory errors

On Wed, 6 Nov 2019 08:43:50 -0600 Marcin Jurek wrote: > I have very little clue what to do, above all because I don't know > how to reproduce the error. Using AddressSanitizer to find memory errors in R packages requires the R installation to be built with AddressSanitizer, too. I found it

Re: [R-pkg-devel] potential memory leak using openMP

On Fri, 15 Nov 2019 10:49:25 -0600 Marcin Jurek wrote: > 1) what should I do to reproduce the error? The following is a quick, unchecked suggestion, but: `R CMD check --use-valgrind` just adds `-d valgrind` to the command line, while the report you are seeing can only be obtained with

Re: [R-pkg-devel] Fix non-ASCII characters in R packages

On Mon, 2 Dec 2019 10:57:51 -0300 Rafael Pereira wrote: > checking data for non-ASCII characters ... NOTE Note: found 58 marked > Latin-1 strings > > I have used to code below to identify my scripts that have strings > using non-ASCII characters. I don't think it's about non-ASCII in source

Re: [R-pkg-devel] checking CRAN incoming feasibility NOTE

On Sat, 5 Oct 2019 16:52:16 -0500 "R. Mark Sharp" wrote: > MIT + file LICENSE > File 'LICENSE': > Copyright 2017-2019 R. Mark Sharp > > Permission is hereby granted, <...> Note that for packages licensed under MIT license, the LICENSE file should only contain the lines: >> YEAR:

Re: [R-pkg-devel] Adding .exes to R package?

On Wed, 22 Jan 2020 20:54:40 + Jonathan Greenberg wrote: > Are there reasonable tutorials on how to do this? If you absolutely have to do this, take a look at the tinytex package. It is basically an installer for a preselected set of packages from TeX Live inside a platform-specific

Re: [R-pkg-devel] finding "logo.jpg" [was: "try" malfunctions on Ubuntu Linux 16.04 LTS, R-release, GCC]

On Mon, 3 Feb 2020 13:30:11 -0600 Spencer Graves wrote: > logo.jpg <- paste(R.home(), "doc", "html", "logo.jpg", sep > = .Platform$file.sep) I wonder whether file.path(R.home('doc'), 'html', 'logo.jpg') would be more portable. Are there R installations built without the HTML docs? -- Best

Re: [R-pkg-devel] Catching console messages from libGL

On Mon, 17 Feb 2020 14:56:31 -0500 Duncan Murdoch wrote: > So how do I capture stderr (or, off topic here, how do I get libGL to > be quiet)? libGL seems to only offer bad news in this regard: it writes directly to stderr [1] and does not seem to offer a way to silence the _LOADER_FATAL

Re: [R-pkg-devel] CRAN Package Check Results - No protocol specified (OS X only)

On Mon, 17 Feb 2020 19:28:43 -0500 Dominic Comtois wrote: > a bunch of warnings with "No protocol specified" messages "No protocol specified" is printed by the X11 client library when it fails to connect to the X server. I think that these indicate a problem with setup of the macOS testing

Re: [R-pkg-devel] Error in curl: Failed FTP upload: 550

On Fri, 21 Feb 2020 14:04:24 +0100 Gianmarco Alberti wrote: > I have also used: > check_win_devel() and check_win_release() out of devtools, but I keep > getting the following message: > Error in curl::curl_fetch_memory(url, handle = h) : > Failed FTP upload: 550 Does it work if you build the

Re: [R-pkg-devel] Need help to resolve NOTEs in auto check

Hello Ian, On Wed, 22 Jan 2020 10:29:51 + Ian Walker wrote: > * checking CRAN incoming feasibility ... NOTE > Maintainer: ‘Ian Walker < > i.wal...@bath.ac.uk > >’ This NOTE is there for CRAN staff to have another look at the Maintainer: field in case this is someone's first submission or

Re: [R-pkg-devel] For reproducibility issue

On Fri, 17 Jan 2020 13:55:39 + وليد خلف معوض المطيرى wrote: > So, does anyone have an idea of how to solve this issue. "Writing R Extensions", 1.6. Writing portable packages: >> Compiled code should not call the system random number generators >> such as rand, drand48 and random, but

Re: [R-pkg-devel] Checkpoint package failing CRAN checks

I wonder why does vignettes/checkpoint.Rmd run the following: > example_project <- tempdir() Now example_project contains the path of per-session temporary directory... > dir.create(example_project, recursive = TRUE, showWarnings = FALSE) ...so there should be no need to create it... >

Re: [R-pkg-devel] rhub, docker and Bioconductor

On Tue, 7 Jan 2020 13:54:38 + Christian Martin Hennig wrote: > Are there any other options apart from rhub/docker to get wiser about > my errors and issues (error on debian-clang in a routine that shows > nothing suspicious on my machine I cannot answer your original questions, but I can

Re: [R-pkg-devel] suggestion: conda for third-party software

On Tue, 7 Jan 2020 15:49:45 +0100 Serguei Sokol wrote: > Currently, many R packages include TPS as part of them thus bloating > their sizes and often duplicating files on a given system.  And even > when TPS is not included in an R package but is just installed on a > system, it is not so

Re: [R-pkg-devel] Installed package size

On Thu, 12 Mar 2020 15:16:13 + Carsten Croonenbroeck wrote: > I would like to know what's the maximum size and if there's a way > around that limit. Here's what CRAN policy [*] says about that: >> As a general rule, neither data nor documentation should exceed 5MB >> (which covers several

Re: [R-pkg-devel] An invalid URLs

On Fri, 13 Mar 2020 09:49:03 +0800 (GMT+08:00) jared_wood wrote: > Status: 403 > > Message: Forbidden > > > > I don’t know why. The URL was picked up in the article of this > database and I can open it. To be fair, my requests to this service are also blocked unless I use Tor

Re: [R-pkg-devel] More GitHub problems

On Mon, 20 Apr 2020 23:44:43 -0500 Spencer Graves wrote: > Is there a way to restore the functionality of a local clone of a > GitHub repository after the SSH key it used was replaced? Does `git remote -v` in the repo directory show https://github.com/... or g...@github.com:... or ssh://...

Re: [R-pkg-devel] An invalid URLs

On Fri, 13 Mar 2020 11:02:06 +0300 Ivan Krylov wrote: > the remote server could deny requests from such automated user > agents, only allowing clients that look like browsers Here is what I have been able to observe: If wait for some time, then try to access http://www.malacards.org/

Re: [R-pkg-devel] /usr/bin/ld: cannot find -ludev

On Sun, 26 Apr 2020 15:39:50 + "Sameh M. Abdulah" wrote: > Yes, I think I will need it Could you tell us why your package needs it? Perhaps there is a way to make it an optional dependency. > since I know that this is an OS libs It is true that libudev is required for successful bootup of

Re: [R-pkg-devel] Help Debugging Debian Error

On Fri, 15 May 2020 03:50:12 -0400 Paul Hibbing wrote: > Complete output: > > library(testthat) > > library(PAutilities) > > > > test_check("PAutilities") It seems to me that the R process crashes while running your tests, but since testthat::test_check captures everything to

Re: [R-pkg-devel] OpenMP variable not specified in enclosing 'parallel'

On Mon, 23 Mar 2020 15:29:20 +0100 Emil Sjørup wrote: > const int iMaxLag = 20; > error: ‘iMaxLag’ not specified in enclosing ‘parallel’ > error: ‘iMaxLag’ is predetermined ‘shared’ for ‘shared’ This looks like a compiler bug to me. g++ seems to forget the rule that "const" variables are

[R-pkg-devel] Guidelines on use of snow-style clusters in R packages?

Some of the packages I use make it possible to run some of the computations in parallel. For example, sNPLS::cv_snpls calls makeCluster() itself, makes sure that the package is loaded by workers, exports the necessary variables and stops the cluster after it is finished. On the other hand,

Re: [R-pkg-devel] Etiquette for package submissions that do not automatically pass checks?

Dear Cesko, On Fri, 14 Aug 2020 21:08:55 +0200 Cesko Voeten wrote: > The package contains functionality to run on cluster nodes that were > set up by the user and needs to access its own internal functions > from there. Apologies for derailing the thread, but I had a similar problem a few

Re: [R-pkg-devel] Formatting .Rbuildignore

On Mon, 17 Aug 2020 15:56:07 +0200 Thierry Onkelinx wrote: > Can we add blank lines in .Rbuildignore? Or lines with only comments > (line starting with #)? .Rbuildignore is not documented [1] to allow comments, but the current implementation does skip empty lines [2] since 2010 [3] (otherwise

Re: [R-pkg-devel] How to retrieve a flag set in configure.ac (filled in Makevars.in) during package installation in an R or C++ script ?

On Sat, 15 Aug 2020 19:50:41 +0530 Akshit Achara wrote: > To access these files, I need to use the path of libminizinc (which > can change per installation). I want to extract this path from either > Makevars or configure to use it in my package. Just as Makevars is generated during

Re: [R-pkg-devel] "non-ASCII input" and "--data-compress" ignored

On Fri, 17 Jul 2020 02:02:36 -0500 Spencer Graves wrote: > If I copy this URL into a browser and back out again, I get > the following: > > > https://www.americansecurityproject.org/ASP%20Reports/Ref%200072%20-%20North%20Korea%E2%80%99s%20Nuclear%20Program%20.pdf > > >   However, if I

Re: [R-pkg-devel] data and load version 3

On Mon, 29 Jun 2020 22:55:02 +0200 Göran Broström wrote: > After googling for a while (found nothing relevant in 'WRE'), I > understand that I have two options: (i) Change 'Depends' in > DESCRIPTION as suggested, and (ii) using save with 'version = 2' for > the new files. One of the steps

Re: [R-pkg-devel] data and load version 3

On Tue, 30 Jun 2020 11:48:29 +0200 Göran Broström wrote: > No point at all with version 3 in packages? Format version 3 [1] introduces support for ALTREP objects [2]. Examples of where ALTREP might be useful include really long integer vectors, like 1:1e10. -- Best regards, Ivan [1]

Re: [R-pkg-devel] package installation and linking with JAGS

On Wed, 8 Jul 2020 11:06:31 +0200 Frantisek Bartos wrote: >Check: for GNU extensions in Makefiles, Result: WARNING This warning is easy to deal with: >JAGS_ROOT ?= c:/progra~1/JAGS/JAGS-4.3.0 Use plain "=" macro definitions, since others aren't considered portable enough. >SOURCES=

Re: [R-pkg-devel] Valgrind warning on saveRDS, about object in external pointer

On Wed, 08 Jul 2020 19:23:41 +0300 David Cortes wrote: >- The warning is about an un-initialized value allocated in a call to >C++ std::vector::reserve, which is called on a C++ vector member of the >struct in the external pointer. I'm ready to admit that I didn't read the code well enough, but

Re: [R-pkg-devel] warning: type of ‘zhpevx_’ does not match original declaration [-Wlto-type-mismatch]

On Tue, 7 Jul 2020 03:00:23 + Pierre Lafaye de Micheaux wrote: >Should I just write something like (adding the middle instruction >below to my existing code above)?: > >#ifdef FC_LEN_T >typedef long long int FC_LEN_T; No, I don't think that would help. What _might_ help is adapting the

Re: [R-pkg-devel] Valgrind warning on saveRDS, about object in external pointer

On Wed, 08 Jul 2020 22:43:13 +0300 David Cortes wrote: > About the source code: it actually complains about line > fit_model.cpp:751 : > hplane_root->reserve(exp_nodes); My fault. I was reading the GitHub source code instead of CRAN package source code. > I’m not able to reproduce the warning

Re: [R-pkg-devel] warning: type of ‘zhpevx_’ does not match original declaration [-Wlto-type-mismatch]

On Fri, 3 Jul 2020 00:15:27 + Pierre Lafaye de Micheaux wrote: >Found the following significant warnings: >myzhpevx.cpp:13:23: warning: type of _zhpevx__ does not match > original declaration [-Wlto-type-mismatch] I managed to reproduce the warning on R-devel r78607 built with

Re: [R-pkg-devel] how to prevent a small package from yielding a large installed size?

On Mon, 15 Jun 2020 11:13:21 + Daniel Kelley wrote: > A possible clue is that I get a large-file note on macOS, but not > when I use rhub for test linux builds, or winbuilder for a windows > build. I do not have ready access to either linux or windows > machines, to examine those builds in

Re: [R-pkg-devel] package CatDataAnalysis

On Sun, 28 Jun 2020 11:07:46 -0500 Charles Geyer wrote: >Please note that I made Alan Agresti (with his acquiescence) the >author of the package Sorry to derail this, but is it possible for Alan Agresti to add a line to the page [*] allowing redistribution of the data, preferably under the

Re: [R-pkg-devel] R package does not find DLL routine

On Sun, 28 Jun 2020 12:43:53 +0200 Lisa GM wrote: > "sum_c" not resolved from current namespace (sum) As mentioned by Dirk Eddelbuettel, this is not the way R packages are supposed to be built [*], but if you are absolutely positive you cannot build the DLL from source together with the

Re: [R-pkg-devel] [External] Guidelines on use of snow-style clusters in R packages?

On Wed, 3 Jun 2020 08:54:56 -0500 (CDT) luke-tier...@uiowa.edu wrote: > If you use [a cluster] passed to you it would be best to leave > it in the state you found it at least as far as the search path and > global environment are concerned. Thanks for this advice! I guess that clusterExport() is

Re: [R-pkg-devel] [R] a question of etiquette

On Tue, 2 Jun 2020 20:33:56 -0400 Avraham Adler wrote: > If there is a term which reflects that mechanism from a discipline > other than biology, please let me know. I think that "copyleft" is the term you are looking for. The Wikipedia page [*] defines it as >> the practice of offering people

Re: [R-pkg-devel] Note: information on .o files is not available / Found '_exit', possibly from '_exit' (C)

On Fri, 17 Jul 2020 11:25:40 +0200 Fabio Sigrist wrote: > Found '_exit', possibly from '_exit' (C) > Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) > Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) > Found 'printf', possibly from 'printf' (C) A curious

Re: [R-pkg-devel] os/x compiled w/ openmp?

On Mon, 13 Jul 2020 10:14:14 -0400 Joshua N Pritikin wrote: > Is this the best place to ask? R-SIG-Mac [*] is probably a better place for this. The short answer is that OpenMP support has been dropped from the compiler supplied with macOS, but there are workarounds [**]. -- Best regards, Ivan

Re: [R-pkg-devel] "non-ASCII input" and "--data-compress" ignored

On Fri, 17 Jul 2020 18:08:24 -0500 Spencer Graves wrote: >   I tried escaping "%" every time it occurred without success, > but adding "\encoding{UTF-8}" as the 4th line of > nuclearWeaponStates.Rd eliminated that problem. Glad it works for you, but you might want to check that the link

Re: [R-pkg-devel] [Re] warning: type of ‘zhpevx_’ does not match original declaration [-Wlto-type-mismatch]

Dear Pierre L., I think that the zhpevxC wrapper, as written, may result in undefined behaviour: >const char *JOBZ = jobz[0]; >delete[] JOBZ; >delete[] Cap; This could work okay, depending on how the rest of the package is written, but in general, it is considered a bad idea for

Re: [R-pkg-devel] FW: [CRAN-pretest-archived] CRAN submission valmetrics 1.0.0

On Wed, 16 Dec 2020 07:12:04 + Kristin Piikki wrote: > Check: PDF version of manual, Result: WARNING > LaTeX errors when creating PDF version. > This typically indicates Rd problems. > LaTeX errors found: > ! Package inputenc Error: Unicode char ‐ (U+2010) > (inputenc)

Re: [R-pkg-devel] Sudden error on r-devel-windows-ix86+x86_64

On Thu, 14 Jan 2021 12:41:02 +0100 Helmut Schütz wrote: > Any ideas what might be the reason? This happened yesterday to one of my packages, with a similarly cryptic error page (just an "r" instead of a log), then got better by itself by today. Most likely, some problems on the test machine.

Re: [R-pkg-devel] Rdmacros as Suggests rather than Imports

On Sat, 23 Jan 2021 04:54:51 -0500 Duncan Murdoch wrote: > I wonder if there's a way to define stubs for the macros in the > package, and use mathjaxr versions only conditional on having it > available? I had an idea along the lines of \Sexpr[results=rd]{if (...) '\\newcommand{\\mjeqn}{...}'}

[R-pkg-devel] Debugging M1mac problems

Dear R-package-devel, My package "albatross" doesn't contain any compiled code and has been checked on both a POSIX-compatible system and on Windows, so I wasn't expecting any problems after seeing it pass CRAN "pretest" checks. Imagine my surprise when it failed a test on M1mac while reading

Re: [R-pkg-devel] Debugging M1mac problems

Dirk, thank you a prompt reply! I see the issue you took part in solving: https://github.com/x13org/x13binary/issues/49 Wondering if a combination of environment variables for R CMD check could have helped reproduce this on another machine. Unfortunately

Re: [R-pkg-devel] FW: CRAN submission RIBMDB 1.0-21

On Tue, 23 Feb 2021 02:03:34 + Binit Kumar wrote: > I uploaded a package to CRAN but didn’t get any response on success > or failure. How to know the status of the same? Glad to know you were able to solve the check problems! Your package is currently waiting in the queue to be

Re: [R-pkg-devel] Debugging M1mac problems [solved]

On Sat, 27 Mar 2021 17:26:16 +0300 Ivan Krylov wrote: > I'm probably doing something stupid with the file names that usually > works but isn't guaranteed to work in all cases, but I cannot figure > it out. Long story short, the problem turned out to be that I called basename() an

Re: [R-pkg-devel] How to R CMD build / check using LTO

On Wed, 17 Feb 2021 20:04:34 +0100 Paul Schmidt-Walter wrote: > I simply don't know how to "build with configure --enable-lto" "R Installation and Administration" contains a detailed set of instructions on how to compile R,

Re: [R-pkg-devel] FW: [CRAN-pretest-archived] CRAN submission RIBMDB 1.0.0

Hello Binit Kumar, On Wed, 17 Feb 2021 15:12:53 + Binit Kumar wrote: > Error: Ld:/Compiler/gcc-4.9.3/local330/lib > -LD:/RCompile/recent/R/bin/i386 -lR clidriver/bin/db2app64.dll: file > not recognized: file format not recognized > > Why is db2app64.dll a non recognized file? The package

Re: [R-pkg-devel] FW: [CRAN-pretest-archived] CRAN submission RIBMDB 1.0.0

On Thu, 18 Feb 2021 02:37:22 + Binit Kumar wrote: > 1. Windows: As I can see in the logs of the machine: > > platform = windows , arch = x64 , R_Version = R Under development > (unstable) (2021-02-16 r80015) We might need the help of someone else more knowledgeable of Windows package

Re: [R-pkg-devel] Error occurring only when I submit to CRAN

On Fri, 12 Feb 2021 02:45:02 -0500 Elysée Aristide wrote: > How can I fix this given that I am not able to reproduce the error > locally? Your LaTeX setup seems to have better Unicode support than the one installed on CRAN machines. Try using tools::showNonASCIIfile on all your *.Rd files to

Re: [R-pkg-devel] UX for "WARNING unable to translate to native encoding"?

On Mon, 16 Aug 2021 09:05:54 + David Norris wrote: > Unicode U+00d7 (times), U+00b1 (plus-minus) and U+03bc (mu) have > equivalents in Latin-1 encoding, and I have used these without > difficulty in strings, neither U+2206 (INCREMENT) nor U+0394 (Greek > Delta) does But not in some other

Re: [R-pkg-devel] http error handling in packages

On Wed, 8 Sep 2021 12:02:51 +1200 obrl soil wrote: > I just want to clarify whether the problem is an overly brief error > message, or my use of stop() in this context? I think it's neither: it's perfectly fine to use the R error system to signal being unable to establish function

Re: [R-pkg-devel] can't reproduce 'Additional issues' on CRAN with valgrind

On Mon, 2 Aug 2021 17:11:14 + Georgi Boshnakov wrote: > What am I missing? Do I need to have a separate library for the > instrumented R-devel version? It doesn't look to me like you're missing anything, unless you start seeing the errors when you start `R -d valgrind` and then run the

Re: [R-pkg-devel] Ongoing CXX17 woes

On Fri, 6 Aug 2021 15:51:37 -0500 Tim Keitt wrote: > CXX17=`${R_HOME}/bin/R CMD config --all | awk '{print $1}' | grep \ > "^CXX17$"` This seems to output "CXX17" on a machine with no C++17 support. On the other hand, running `${R_HOME}/bin/R CMD config CXX17` here gives me an empty string. --

Re: [R-pkg-devel] Internet resources and Errors

On Fri, 24 Sep 2021 07:49:44 -0700 Roy Mendelssohn - NOAA Federal via R-package-devel wrote: > All internet calls are wrapped in 'try()'. If that shows an error, > I write a message to the screen about the error, and call stop(), > perhaps with a further message in that call. Somehow this

Re: [R-pkg-devel] multithreading in packages

В Thu, 7 Oct 2021 21:58:08 -0400 (EDT) Vladimir Dergachev пишет: >* My understanding from reading documentation and source code is > that there is no dedicated support in R yet, but there are packages > that use multithreading. Are there any plans for multithreading > support in future R

Re: [R-pkg-devel] Tests run without --as-cran and not with

On Fri, 24 Sep 2021 21:48:12 +0200 Jan van der Laan wrote: > my tests run fine when run with R CMD check, but not with R CMD check > --as-cran <...> > pandoc then calls R again with a script which is part of the package Part of R CMD check --as-cran is placing fake R and Rscript executables

Re: [R-pkg-devel] Checking package in Windows fails

On Mon, 15 Nov 2021 17:15:14 +0100 Ben Engbers wrote: > I don't know why I have to explicitly include 'library("rex")' in > the code since I have added rex to the Imports in the DESCRIPTION Have you added the corresponding importFrom(...) [1] commands to your NAMESPACE file? > pi <-

Re: [R-pkg-devel] CRAN submission error when running tests in testthat

On Wed, 24 Nov 2021 16:37:44 + (UTC) Nathan Green via R-package-devel wrote: > An irrecoverable exception occurred. R is aborting now ... It seems that some of your dependencies which use compiled code manage to crash the R process on CRAN Mac machines. Since testthat normally hides most

Re: [R-pkg-devel] CRAN submission error when running tests in testthat

On Thu, 25 Nov 2021 12:33:01 +0100 Gábor Csárdi wrote: > Are you sure about this? I don't think testthat hides any output. R > CMD check on the other hand AFAICT only shows the last 13 lines by > default. See the _R_CHECK_TESTS_NLINES_ environment variable in >

Re: [R-pkg-devel] Checking package in Windows fails

On Wed, 17 Nov 2021 00:20:44 +0100 Ben Engbers wrote: > I don't edit the NAMESPACE file by hand. It is created by roxygen2. Right. In that case, use an @importFrom tag: https://roxygen2.r-lib.org/articles/namespace.html#imports -- Best regards, Ivan

Re: [R-pkg-devel] Cannot find source of devtool::check() warnings in R code

On Thu, 9 Dec 2021 11:10:36 -0500 Steve Gutreuter wrote: > Warning: replacing previous import ‘pROC::cov’ by ‘stats::cov’ > when loading ‘screenr’ > Warning: replacing previous import ‘pROC::var’ by ‘stats::var’ > when loading ‘screenr’ > Warning: replacing previous import

Re: [R-pkg-devel] Different behavior from devtools::check and install.packages() under Linux and Windows

On Tue, 14 Dec 2021 08:48:23 -0500 Steve Gutreuter wrote: > Error in set_makevars(.new, .path, makevars_file, assignment = > .assignment) : >   Multiple results for CXX11FLAGS found, something is wrong.FALSE set_makevars is a function from the "withr" package:

Re: [R-pkg-devel] table lacks "summary" attribute

On Sat, 5 Mar 2022 16:54:08 -0800 alexios galanos wrote: > * checking HTML version of manual ... NOTE > Found the following problems: > DCCfilter-class.Rd:7:1: Warning: lacks "summary" attribute > > Any pointers/documentation on this? This seems to be the new check for HTML documentation

Re: [R-pkg-devel] should I increase the version number when resubmitting a package that failed incoming tests?

On Thu, 17 Feb 2022 20:53:50 + Daniel Kelley wrote: > My question is: should I retain the same version number, or should I > bump the number? CRAN policy currently says: "Increasing the version number at each submission reduces confusion so is preferred even when a previous submission was

Re: [R-pkg-devel] What is best practice for handling false negatives on CRAN submission tests?

On Sat, 19 Mar 2022 12:14:30 + Daniel Kelley wrote: > Would I be sensible to wait a couple of weeks for a reply? I agree with Duncan, I'd wait for days, not weeks. > I ask because the schedule would have oce being auto-removed from > CRAN early next month, and I worry a bit about that

Re: [R-pkg-devel] Possible bug report/false positive

On Wed, 5 Jan 2022 17:15:20 -0300 Igor L wrote: > Found the platform-specific device: >'X11' > how to solve it? One of the tricks that work (in the sense that calls to functions using non-standard evaluation don't result in warnings about "Undefined global functions or variables") is to

Re: [R-pkg-devel] handling of byte-order-mark on r-devel-linux-x86_64-debian-clang machine

On Tue, 5 Apr 2022 20:20:37 +0200 Tomas Kalibera wrote: > I've rewritten the paragraphs, biasing towards users who have UTF-8 > as the native encoding as this is going to be the majority. Thank you! > But the level of detail I think needs to remain as long as these > features are supported -

Re: [R-pkg-devel] Modernizing legacy Fortran:, REAL(kind=8)

On Wed, 30 Aug 2023 08:43:04 +0200 Thomas Petzoldt wrote: > a) change REAL(kind=8) back to DOUBLE PRECISION that is again old > style. It seems to be portable and is still widely used. I don't have a reference as good as the Fortran standard, but Steve Lionel said in Dr. Fortran [*] that DOUBLE

Re: [R-pkg-devel] CRAN Detected Using More Than 2 Cores By Default

В Fri, 1 Sep 2023 08:26:32 -0400 Matt Dancho пишет: > Check: tests, Result: NOTE > Running 'testthat.R' [20s/7s] >Running R code in 'testthat.R' had CPU time 2.7 times elapsed time > > Flavor: r-devel-linux-x86_64-debian-gcc > Check: re-building of vignette outputs, Result: NOTE >

Re: [R-pkg-devel] Python module dependency

On Fri, 1 Sep 2023 08:14:12 + Hanyu Song wrote: > b. I read from the documentation of the R package "reticulate" that > we should delay load the Python modules, but it is not entirely clear > to me how to do it. > Do I need to create any virtual environment? Not in the package code (unless

Re: [R-pkg-devel] How to fix Archived Package Rpdb?

13 сентября 2023 г. 18:01:56 UTC, Leonard Mada via R-package-devel пишет: >Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = >TRUE,  : >  arguments imply differing number of rows: 1, 0 This is a bug in devtools where a value originating from subsetting a list using

Re: [R-pkg-devel] fortran integer(kind=)

On Thu, 31 Aug 2023 06:52:47 + Berry Boessenkool wrote: > my R package dwdradar uses Fortran code with the input parameter > integer(KIND=2): > https://github.com/brry/dwdradar/blob/master/src/binary_to_num.f90#L20 > https://github.com/brry/dwdradar/blob/master/src/binary_to_num.f90#L55 The

Re: [R-pkg-devel] published CRAN check results give error for only r-oldrel-macos-arm64

On Fri, 13 Oct 2023 09:11:20 + Tony Wilkes wrote: > My R package has yesterday been accepted by CRAN. I'm super happy > about this, of course. But when I look at the package's CRAN check > results (see > https://cran.r-project.org/web/checks/check_results_tinycodet.html), > I see that

Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission

Dear Sylvain, В Tue, 17 Oct 2023 09:45:25 + (UTC) "cartograf...@gmail.com" пишет: > I've uploaded cartogRaflow version 1.0.4 with sf package.  > I've submitted yesterday the version 1.0.4 in CRAN and received 2 two > error message because cartogRaflow is archived and use rgeos maptools > in

Re: [R-pkg-devel] CartogRaflow submission

On Mon, 16 Oct 2023 21:38:59 + (UTC) "cartograf...@gmail.com" wrote: > Hi, I've put an update version of the package cartogRaflow 1.0.4 in > CRAN today. What was the full check result? > Last released version's CRAN status: OK: 11, ERROR: 2 > See: >

Re: [R-pkg-devel] CartogRaflow submission

This is the NOTE you've been asked to fix: > * checking installed files from ‘inst/doc’ ... NOTE > The following files should probably not be installed: > ‘Logo_cartograflow.png’ > > Consider the use of a .Rinstignore file: see ‘Writing R Extensions’, > or move the vignette sources from

[R-pkg-devel] RFC: an interface to manage use of parallelism in packages

Summary: at the end of this message is a link to an R package implementing an interface for managing the use of execution units in R packages. As a package maintainer, would you agree to use something like this? Does it look sufficiently reasonable to become a part of R? Read on for why I made

Re: [R-pkg-devel] "crossprod" is not a BUILTIN function

В Wed, 25 Oct 2023 21:02:00 +0200 Plamen Mirazchiyski пишет: > Today I was preparing a new version for the RALSA package. I have > built a Windows package using "devtools::check_win_devel()". > The machine has R 4.3.1, the latest official release. After I load the > test RALSA package, R

Re: [R-pkg-devel] Issue with R Package on CRAN - OpenMP and clang17

В Thu, 2 Nov 2023 10:38:56 +0100 (CET) Romain Pierlot пишет: > Does a compiler bug imply that the issue doesn't come from from the > code? Yes. I'm sure (corrections welcome!) that it's not an error to use a Fortran variable before an OpenMP parallel block that also uses it for a reduction

Re: [R-pkg-devel] Unclear NOTE for r-devel-linux-x86_64-debian-clang

On Thu, 2 Nov 2023 07:58:12 + Tony Wilkes wrote: > pkgs.html:66:9 (pkgs.Rd:24): Warning: anchor "pkgs" already > defined Looks like the same problem as here: https://stat.ethz.ch/pipermail/r-package-devel/2023q4/009790.html Should have been fixed in SVN r85440. Unfortunately, the check

Re: [R-pkg-devel] Issue with R Package on CRAN - OpenMP and clang17

В Mon, 30 Oct 2023 18:52:29 +0300 Ivan Krylov пишет: > I'll try to reproduce your problem, starting by downloading and > compiling flang from https://github.com/llvm/llvm-project.git commit > 092b6c5ee3707ea10b9f10d0a674e8d12395369b (as stated at > <https://www.stats.ox.ac.uk/

Re: [R-pkg-devel] RFC: an interface to manage use of parallelism in packages

В Wed, 25 Oct 2023 13:54:53 -0700 "Reed A. Cartwright" пишет: > For a comparison, I'd recommend looking at how GNU make does parallel > processing. It uses the concept of job server and job slots. What I > like about it is that it is implemented at the OS level because make > needs to support

Re: [R-pkg-devel] DLL requires the use of native symbols

Dear Simon, Could you please look into this? The machines running r-release-macos-* checks seem to have MassSpecWavelet < 1.66 installed instead of the current version, 1.68. I think that MassSpecWavelet >= 1.66 would be version-appropriate for R-4.3 (Bioconductor >= 3.17). On Tue, 31 Oct 2023

Re: [R-pkg-devel] "crossprod" is not a BUILTIN function

В Thu, 26 Oct 2023 15:43:54 +0200 Plamen Mirazchiyski пишет: > If I understand Ivan's email, my package should work on R 4.3.1, but > what about newer versions? The source package (the .tar.gz file obtained using R CMD build) will keep working fine on both R 4.3 and R 4.4. The binary package

Re: [R-pkg-devel] API client package failing due to API authentication

В Thu, 26 Oct 2023 11:14:15 -0400 Cole Johanson пишет: > I have wrapped the examples with the roxygen2 tag *\dontrun*, but it > is still attempting to run the examples. Judging by the latest commit at

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